The Super-K is located underground in Kamioka Mining and Smelting Co.'s Mozumi Mine in Hida's Kamioka area. It consists of a cylindrical stainless steel tank that is tall and in diameter holding 50,000 tons of ultra-pure water. The tank volume is divided by a stainless steel superstructure into an inner detector (ID) region that is in diameter and in height and outer detector (OD) which consists of the remaining tank volume. Mounted on the superstructure are 11,146 photomultiplier tubes (PMT) in diameter that face the ID and 1885 PMTs that face the OD. There is a barrier that optically separates the ID and OD.

A neutrino interaction with the electrons or nuclei of water can produce a charged particle that moves faster than the speed of light in water (although of course slower than the speed of light in vacuum). This creates a cone of light known as Cherenkov radiation, which is the optical equivalent to a sonic boom. The Cherenkov light is projected as a ring on the wall of the detector and recorded by the PMTs. Using the timing and charge information recorded by each PMT, the interaction vertex, ring direction and flavor of the incoming neutrino is determined. From the sharpness of the edge of the ring the type of particle can be inferred. The multiple scattering of electrons is large, so electromagnetic showers produce fuzzy rings. Highly relativisticmuons, in contrast, travel almost straight through the detector and produce rings with sharp edges.

The detector, named KamiokaNDE for Kamioka Nucleon Decay Experiment, was a tank in height and in width, containing 3,000 tons of pure water and about 1,000 photomultiplier tubes (PMTs) attached to its inner surface. The detector was upgraded, starting in 1985, to allow it to observe solar neutrinos. As a result, the detector (KamiokaNDE-II) had become sensitive enough to detect neutrinos from SN 1987A, a supernova which was observed in the Large Magellanic Cloud in February 1987, and to observe solar neutrinos in 1988. The ability of the Kamiokande experiment to observe the direction of electrons produced in solar neutrino interactions allowed experimenters to directly demonstrate for the first time that the sun was a source of neutrinos.

Despite successes in neutrino astronomy and neutrino astrophysics, Kamiokande did not achieve its primary goal, the detection of proton decay. Higher sensitivity was also necessary to obtain high statistical confidence in its results. This led to the construction of Super-Kamiokande, with fifteen times the water and ten times as many PMTs as Kamiokande. Super-Kamiokande started operation in 1996.

The Super-Kamiokande Collaboration announced the first evidence of neutrino oscillation in 1998. This was the first experimental observation consistent with the theory that the neutrino has non-zero mass, a possibility that theorists had speculated about for years.

On November 12, 2001, about 6,600 of the photomultiplier tubes in the Super-Kamiokande detector imploded, apparently in a chain reaction as the shock wave from the concussion of each imploding tube cracked its neighbours. The detector was partially restored by redistributing the photomultiplier tubes which did not implode, and by adding protective acrylic shells that are hoped would prevent another chain reaction from recurring (SuperKamiokande-II).

In July 2005, preparations began to restore the detector to its original form by reinstalling about 6,000 PMTs. The work was completed in June 2006, whereupon the detector was renamed SuperKamiokande-III.